Here, we simulate a representation of molecular evolution of digital organisms (replicators), each of which contains a single piece of DNA.
We engineer a computational method to cartoon the double-stranded structure of DNA, and simulate inversion-like mutations consisting of a permutation of a segment of the complementary strand, which is then exchanged with the main strand segment (see Sec:Methods, schema REF ).
For the sake of simplicity, we consider digital genotypes made up of binary nucleotides
(i.e. a binary alphabet \(\lbrace 0,1\rbrace \)  instead of the four-nucleotides alphabet \(\lbrace \mathtt {A,T,C,G}\rbrace \) ).
The sequences are arranged in circular strings with constant number of base-pairs.
In an abstract sense, the model mimics the molecular evolution of some viruses [1]} and (animal) mitochondrial DNA [2]} with compact genomes and closed double-stranded DNA circles [1]}, [4]}, [5]}.
It is very important to emphasise that our computational model simulates intragenic-like mutations [6]}, [7]}, [8]}.
We are modelling asexual replication, therefore recombination is not considered.
To build rugged fitness landscapes, we adopt the well known Kauffman NK model, where N denotes the length of the genome and \(\textrm {K}\)  parameterizes the “epistatic” coupling between nucleotides [9]}, [10]}, [11]}, [12]}.
We do not include environmental changes, so the landscape remains constant through the simulations.
Finally, it is worth mentioning that all our simulations were conducted in the evolutionary regime of strong selection weak mutations (SSWM) [13]}.
